diff --git a/rnaseq_pipeline/tasks.py b/rnaseq_pipeline/tasks.py index 4fbfb09b..fa143b96 100755 --- a/rnaseq_pipeline/tasks.py +++ b/rnaseq_pipeline/tasks.py @@ -103,6 +103,7 @@ def run(self): r1.path, join(destdir, os.path.basename(r1.path)), minimum_length=self.minimum_length, + report_file=join(destdir, os.path.basename(r1.path) + '.cutadapt.json'), cpus=4) elif len(self.input()) == 2: r1, r2 = self.input() @@ -113,6 +114,7 @@ def run(self): r2.path, join(destdir, os.path.basename(r2.path)), minimum_length=self.minimum_length, + report_file=join(destdir, os.path.basename(r2.path) + '.cutadapt.json'), cpus=4) elif self.ignore_mate == 'reverse': logger.info('Reverse mate is ignored for %s.', repr(self)) @@ -120,6 +122,7 @@ def run(self): r1.path, join(destdir, os.path.basename(r1.path)), minimum_length=self.minimum_length, + report_file=join(destdir, os.path.basename(r1.path) + '.cutadapt.json'), cpus=4) else: yield platform.get_trim_paired_reads_task( @@ -127,6 +130,7 @@ def run(self): join(destdir, os.path.basename(r1.path)), join(destdir, os.path.basename(r2.path)), minimum_length=self.minimum_length, + report_file=join(destdir, os.path.basename(r1.path) + '_' + os.path.basename(r2.path) + '.cutadapt.json'), cpus=4) else: raise NotImplementedError('Trimming more than two mates is not supported.')